Identification of QTLs and Candidate Genes for Cadmium Tolerance at the Seedling Stage in Rice

Cadmium (Cd) contamination in agricultural soil poses a severe threat to rice growth and food safety worldwide. Seedling-stage Cd tolerance directly determines rice establishment and subsequent yield under Cd stress, but its genetic basis remains largely unclear. In this study, a genome-wide association study (GWAS) was conducted using 490 diverse accessions from the 3000 Rice Genome Project (3K RGP). Three biomass-related traits, shoot height (SH), shoot dry weight (SDW), and root dry weight (RDW), were measured under control and Cd stress conditions, along with their relative values. A total of 3,196,134 high-quality SNPs were used for genetic analysis, and population structure was corrected by principal component analysis (PCA) and kinship matrix. In total, 39 stable QTLs were detected, including 19 for RDW, 18 for SDW, and 2 for SH, most of which were specifically identified under Cd stress. Three major QTLs (qSDW1.1, qRDW3.2, qRDW5.2) were prioritized for candidate gene mining. Combining LD block analysis, gene annotation, Cd-responsive transcriptome data, and haplotype analysis, OsAKR2 (LOC_Os01g62870), OsAS1 (LOC_Os03g18130), and LOC_Os05g11320 were identified as key candidate genes regulating seedling Cd tolerance, and superior haplotypes of these genes were identified. This study reveals the genetic architecture of rice seedling Cd tolerance and provides elite QTLs, genes, and haplotypes for molecular breeding of Cd-resilient rice varieties.